1. ComplexHeatmap
  2. man
  3. anno_oncoprint_barplot.rd
Browse code

generate documentations by pkgdown

Zuguang Gu authored on 18/10/2019 11:34:02
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man/anno_oncoprint_barplot.rd
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deleted file mode 100644
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@@ -1,38 +0,0 @@
1 
-\name{anno_oncoprint_barplot}
2 
-\alias{anno_oncoprint_barplot}
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-\title{
4 
-Barplot Annotation for oncoPrint
5 
-}
6 
-\description{
7 
-Barplot Annotation for oncoPrint
8 
-}
9 
-\usage{
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-anno_oncoprint_barplot(type = NULL, which = c("column", "row"),
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-    bar_width = 0.6, ylim = NULL, axis = TRUE,
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-    axis_param = if(which == "column") default_axis_param("column") else list(side = "top", labels_rot = 0),
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-    width = NULL, height = NULL, border = FALSE)
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-}
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-\arguments{
16 
-
17 
-  \item{type}{A vector of the alteration types in the data. It can be a subset of all alteration types if you don't want to show them all.}
18 
-  \item{which}{Is it a row annotation or a column annotation?}
19 
-  \item{bar_width}{Width of the bars.}
20 
-  \item{ylim}{Data range.}
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-  \item{axis}{Whether draw axis?}
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-  \item{axis_param}{Parameters for controlling axis.}
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-  \item{width}{Width of the annotation.}
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-  \item{height}{Height of the annotation.}
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-  \item{border}{Whether draw the border?}
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-
27 
-}
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-\details{
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-This annotation function should always be used with \code{\link{oncoPrint}}.
30 
-}
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-\author{
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-Zuguang Gu <z.gu@dkfz.de>
33 
-}
34 
-\examples{
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-# There is no example
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-NULL
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-
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-}
Browse code

add jitter argument to Heatmap()

Zuguang Gu authored on 28/09/2019 08:37:13
Showing1 changed files
man/anno_oncoprint_barplot.rd
History View file @9e95ee3
... ... 
@@ -34,4 +34,5 @@ Zuguang Gu <z.gu@dkfz.de>
34 34 
 \examples{
35 35 
 # There is no example
36 36 
 NULL
37 
+
37 38 
 }
Browse code

use pkgdown to build the doc site

Zuguang Gu authored on 24/09/2019 21:01:04
Showing1 changed files
man/anno_oncoprint_barplot.rd
History View file @21aea96
... ... 
@@ -34,5 +34,4 @@ Zuguang Gu <z.gu@dkfz.de>
34 34 
 \examples{
35 35 
 # There is no example
36 36 
 NULL
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-
38 37 
 }
Browse code

add ylim in anno_oncoprint_barplot()

Zuguang Gu authored on 10/06/2019 16:20:21
Showing1 changed files
man/anno_oncoprint_barplot.rd
History View file @9d71409
... ... 
@@ -8,7 +8,7 @@ Barplot Annotation for oncoPrint
8 8 
 }
9 9 
 \usage{
10 10 
 anno_oncoprint_barplot(type = NULL, which = c("column", "row"),
11 
-    bar_width = 0.6, axis = TRUE,
11 
+    bar_width = 0.6, ylim = NULL, axis = TRUE,
12 12 
     axis_param = if(which == "column") default_axis_param("column") else list(side = "top", labels_rot = 0),
13 13 
     width = NULL, height = NULL, border = FALSE)
14 14 
 }
... ... 
@@ -17,9 +17,10 @@ anno_oncoprint_barplot(type = NULL, which = c("column", "row"),
17 17 
   \item{type}{A vector of the alteration types in the data. It can be a subset of all alteration types if you don't want to show them all.}
18 18 
   \item{which}{Is it a row annotation or a column annotation?}
19 19 
   \item{bar_width}{Width of the bars.}
20 
+  \item{ylim}{Data range.}
20 21 
   \item{axis}{Whether draw axis?}
21 22 
   \item{axis_param}{Parameters for controlling axis.}
22 
-  \item{width}{Wisth of the annotation.}
23 
+  \item{width}{Width of the annotation.}
23 24 
   \item{height}{Height of the annotation.}
24 25 
   \item{border}{Whether draw the border?}
25 26
Browse code

set cluster_slice to FALSE for character matrix

Zuguang Gu authored on 18/01/2019 10:43:26
Showing1 changed files
man/anno_oncoprint_barplot.rd
History View file @69345c7
... ... 
@@ -33,4 +33,5 @@ Zuguang Gu <z.gu@dkfz.de>
33 33 
 \examples{
34 34 
 # There is no example
35 35 
 NULL
36 
+
36 37 
 }
Browse code

add NEWs

Zuguang Gu authored on 30/12/2018 08:12:22
Showing1 changed files
man/anno_oncoprint_barplot.rd
History View file @948414f
... ... 
@@ -33,5 +33,4 @@ Zuguang Gu <z.gu@dkfz.de>
33 33 
 \examples{
34 34 
 # There is no example
35 35 
 NULL
36 
-
37 36 
 }
Browse code

update

Zuguang Gu authored on 30/10/2018 08:58:14
Showing1 changed files
man/anno_oncoprint_barplot.rd
History View file @0bb5000
... ... 
@@ -7,17 +7,21 @@ Barplot Annotation for oncoPrint
7 7 
 Barplot Annotation for oncoPrint
8 8 
 }
9 9 
 \usage{
10 
-anno_oncoprint_barplot(type = all_type, which = c("column", "row"),
11 
-    width = NULL, height = NULL, border = FALSE, ...)
10 
+anno_oncoprint_barplot(type = NULL, which = c("column", "row"),
11 
+    bar_width = 0.6, axis = TRUE,
12 
+    axis_param = if(which == "column") default_axis_param("column") else list(side = "top", labels_rot = 0),
13 
+    width = NULL, height = NULL, border = FALSE)
12 14 
 }
13 15 
 \arguments{
14 16
15 17 
   \item{type}{A vector of the alteration types in the data. It can be a subset of all alteration types if you don't want to show them all.}
16 18 
   \item{which}{Is it a row annotation or a column annotation?}
19 
+  \item{bar_width}{Width of the bars.}
20 
+  \item{axis}{Whether draw axis?}
21 
+  \item{axis_param}{Parameters for controlling axis.}
17 22 
   \item{width}{Wisth of the annotation.}
18 23 
   \item{height}{Height of the annotation.}
19 24 
   \item{border}{Whether draw the border?}
20 
-  \item{...}{Other parameters passed to \code{\link{anno_barplot}}.}
21 25
22 26 
 }
23 27 
 \details{
Browse code

documentation checked

Zuguang Gu authored on 23/10/2018 19:59:12
Showing1 changed files
man/anno_oncoprint_barplot.rd
History View file @3c40a7c
... ... 
@@ -1,10 +1,10 @@
1 1 
 \name{anno_oncoprint_barplot}
2 2 
 \alias{anno_oncoprint_barplot}
3 3 
 \title{
4 
-Barplot annotation for oncoPrint
4 
+Barplot Annotation for oncoPrint
5 5 
 }
6 6 
 \description{
7 
-Barplot annotation for oncoPrint
7 
+Barplot Annotation for oncoPrint
8 8 
 }
9 9 
 \usage{
10 10 
 anno_oncoprint_barplot(type = all_type, which = c("column", "row"),
... ... 
@@ -12,8 +12,8 @@ anno_oncoprint_barplot(type = all_type, which = c("column", "row"),
12 12 
 }
13 13 
 \arguments{
14 14
15 
-  \item{type}{A vector of the alteration types in your data. It can be a subset of all alteration types if you don't want to show them all.}
16 
-  \item{which}{Is ti a row annotation or a column annotation?}
15 
+  \item{type}{A vector of the alteration types in the data. It can be a subset of all alteration types if you don't want to show them all.}
16 
+  \item{which}{Is it a row annotation or a column annotation?}
17 17 
   \item{width}{Wisth of the annotation.}
18 18 
   \item{height}{Height of the annotation.}
19 19 
   \item{border}{Whether draw the border?}
... ... 
@@ -21,7 +21,7 @@ anno_oncoprint_barplot(type = all_type, which = c("column", "row"),
21 21
22 22 
 }
23 23 
 \details{
24 
-This annotation function should always use with \code{\link{oncoPrint}}.
24 
+This annotation function should always be used with \code{\link{oncoPrint}}.
25 25 
 }
26 26 
 \author{
27 27 
 Zuguang Gu <z.gu@dkfz.de>
Browse code

fix some bugs

Zuguang Gu authored on 19/10/2018 19:08:59
Showing1 changed files
man/anno_oncoprint_barplot.rd
History View file @864bd88
... ... 
@@ -29,4 +29,5 @@ Zuguang Gu <z.gu@dkfz.de>
29 29 
 \examples{
30 30 
 # There is no example
31 31 
 NULL
32 
+
32 33 
 }
Browse code

update

Zuguang Gu authored on 17/10/2018 06:09:36
Showing1 changed files
man/anno_oncoprint_barplot.rd
History View file @d9834c5
... ... 
@@ -29,5 +29,4 @@ Zuguang Gu <z.gu@dkfz.de>
29 29 
 \examples{
30 30 
 # There is no example
31 31 
 NULL
32 
-
33 32 
 }
Browse code

R CMD check passed

Zuguang Gu authored on 12/10/2018 19:19:48
Showing1 changed files
man/anno_oncoprint_barplot.rd
History View file @b8dacfc
... ... 
@@ -29,4 +29,5 @@ Zuguang Gu <z.gu@dkfz.de>
29 29 
 \examples{
30 30 
 # There is no example
31 31 
 NULL
32 
+
32 33 
 }
Browse code

update

jokergoo authored on 12/10/2018 15:28:37
Showing1 changed files
man/anno_oncoprint_barplot.rd
History View file @1a56796
... ... 
@@ -12,13 +12,16 @@ anno_oncoprint_barplot(type = all_type, which = c("column", "row"),
12 12 
 }
13 13 
 \arguments{
14 14
15 
-  \item{type}{-type}
16 
-  \item{which}{-which}
17 
-  \item{width}{-width}
18 
-  \item{height}{-height}
19 
-  \item{border}{-border}
20 
-  \item{...}{-...}
15 
+  \item{type}{A vector of the alteration types in your data. It can be a subset of all alteration types if you don't want to show them all.}
16 
+  \item{which}{Is ti a row annotation or a column annotation?}
17 
+  \item{width}{Wisth of the annotation.}
18 
+  \item{height}{Height of the annotation.}
19 
+  \item{border}{Whether draw the border?}
20 
+  \item{...}{Other parameters passed to \code{\link{anno_barplot}}.}
21 21
22 
+}
23 
+\details{
24 
+This annotation function should always use with \code{\link{oncoPrint}}.
22 25 
 }
23 26 
 \author{
24 27 
 Zuguang Gu <z.gu@dkfz.de>
... ... 
@@ -26,5 +29,4 @@ Zuguang Gu <z.gu@dkfz.de>
26 29 
 \examples{
27 30 
 # There is no example
28 31 
 NULL
29 
-
30 32 
 }
Browse code

vignette check passed

Zuguang Gu authored on 20/09/2018 22:09:48
Showing1 changed files
man/anno_oncoprint_barplot.rd
History View file @249fdfa
... ... 
@@ -26,4 +26,5 @@ Zuguang Gu <z.gu@dkfz.de>
26 26 
 \examples{
27 27 
 # There is no example
28 28 
 NULL
29 
+
29 30 
 }
Browse code

R CMD check passed

Zuguang Gu authored on 20/09/2018 12:48:08
Showing1 changed files
man/anno_oncoprint_barplot.rd
History View file @ad35494
... ... 
@@ -1,16 +1,24 @@
1 1 
 \name{anno_oncoprint_barplot}
2 2 
 \alias{anno_oncoprint_barplot}
3 3 
 \title{
4 
-Column barplot annotation for oncoPrint
4 
+Barplot annotation for oncoPrint
5 5 
 }
6 6 
 \description{
7 
-Column barplot annotation for oncoPrint
7 
+Barplot annotation for oncoPrint
8 8 
 }
9 9 
 \usage{
10 
-anno_oncoprint_barplot()
10 
+anno_oncoprint_barplot(type = all_type, which = c("column", "row"),
11 
+    width = NULL, height = NULL, border = FALSE, ...)
11 12 
 }
12 
-\details{
13 
-This function is only used for column annotation
13 
+\arguments{
14 
+
15 
+  \item{type}{-type}
16 
+  \item{which}{-which}
17 
+  \item{width}{-width}
18 
+  \item{height}{-height}
19 
+  \item{border}{-border}
20 
+  \item{...}{-...}
21 
+
14 22 
 }
15 23 
 \author{
16 24 
 Zuguang Gu <z.gu@dkfz.de>
... ... 
@@ -18,5 +26,4 @@ Zuguang Gu <z.gu@dkfz.de>
18 26 
 \examples{
19 27 
 # There is no example
20 28 
 NULL
21 
-
22 29 
 }
Browse code

merge by copy paste

Zuguang Gu authored on 17/10/2017 20:55:32
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man/anno_oncoprint_barplot.rd
History View file @1b03a7f
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@@ -1,17 +1,10 @@
1 1 
 \name{anno_oncoprint_barplot}
2 2 
 \alias{anno_oncoprint_barplot}
3 3 
 \title{
4 
-<<<<<<< HEAD
5 4 
 Column barplot annotation for oncoPrint
6 5 
 }
7 6 
 \description{
8 7 
 Column barplot annotation for oncoPrint
9 
-=======
10 
-Column barplot annotaiton for oncoPrint
11 
-}
12 
-\description{
13 
-Column barplot annotaiton for oncoPrint
14 
->>>>>>> bioc/master
15 8 
 }
16 9 
 \usage{
17 10 
 anno_oncoprint_barplot()
Browse code

merge

Zuguang Gu authored on 17/10/2017 19:44:53
Showing0 changed files
Browse code

fix typo

Zuguang Gu authored on 20/08/2017 05:56:30
Showing1 changed files
man/anno_oncoprint_barplot.rd
History View file @e746cf5
... ... 
@@ -1,10 +1,10 @@
1 1 
 \name{anno_oncoprint_barplot}
2 2 
 \alias{anno_oncoprint_barplot}
3 3 
 \title{
4 
-Column barplot annotaiton for oncoPrint
4 
+Column barplot annotation for oncoPrint
5 5 
 }
6 6 
 \description{
7 
-Column barplot annotaiton for oncoPrint
7 
+Column barplot annotation for oncoPrint
8 8 
 }
9 9 
 \usage{
10 10 
 anno_oncoprint_barplot()
Browse code

resove conflict

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@120116 bc3139a8-67e5-0310-9ffc-ced21a209358

Zuguang Gu authored on 14/08/2016 09:20:57
Showing1 changed files
man/anno_oncoprint_barplot.rd
History View file @caada5b
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,22 @@
1 
+\name{anno_oncoprint_barplot}
2 
+\alias{anno_oncoprint_barplot}
3 
+\title{
4 
+Column barplot annotaiton for oncoPrint
5 
+}
6 
+\description{
7 
+Column barplot annotaiton for oncoPrint
8 
+}
9 
+\usage{
10 
+anno_oncoprint_barplot()
11 
+}
12 
+\details{
13 
+This function is only used for column annotation
14 
+}
15 
+\author{
16 
+Zuguang Gu <z.gu@dkfz.de>
17 
+}
18 
+\examples{
19 
+# There is no example
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+NULL
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+
22 
+}
Browse code

removed 'min_gene' in 'oncoPrint()'

Zuguang Gu authored on 03/08/2016 19:36:59
Showing1 changed files
man/anno_oncoprint_barplot.rd
History View file @e979410
... ... 
@@ -18,4 +18,5 @@ Zuguang Gu <z.gu@dkfz.de>
18 18 
 \examples{
19 19 
 # There is no example
20 20 
 NULL
21 
+
21 22 
 }
Browse code

export anno_oncoprint_barplot()

Zuguang Gu authored on 30/06/2016 08:06:47
Showing1 changed files
man/anno_oncoprint_barplot.rd
History View file @0286e38
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,21 @@
1 
+\name{anno_oncoprint_barplot}
2 
+\alias{anno_oncoprint_barplot}
3 
+\title{
4 
+Column barplot annotaiton for oncoPrint
5 
+}
6 
+\description{
7 
+Column barplot annotaiton for oncoPrint
8 
+}
9 
+\usage{
10 
+anno_oncoprint_barplot()
11 
+}
12 
+\details{
13 
+This function is only used for column annotation
14 
+}
15 
+\author{
16 
+Zuguang Gu <z.gu@dkfz.de>
17 
+}
18 
+\examples{
19 
+# There is no example
20 
+NULL
21 
+}